Markov state modeling and dynamical coarse-graining via discrete relaxation path sampling

The Journal of Chemical Physics ◽

10.1063/1.4926940 ◽

2015 ◽

Vol 143 (4) ◽

pp. 044119 ◽

Author(s):

B. Fačkovec ◽

E. Vanden-Eijnden ◽

D. J. Wales

Keyword(s):

Coarse Graining ◽

Path Sampling ◽

Markov State ◽

Markov State Modeling

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Progress in deep Markov State Modeling: Coarse graining and experimental data restraints

The Journal of Chemical Physics ◽

10.1063/5.0064668 ◽

2021 ◽

Author(s):

Andreas Mardt ◽

Frank Noé

Keyword(s):

Experimental Data ◽

Coarse Graining ◽

Markov State ◽

Markov State Modeling

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A Multiscale Perturbation Expansion Approach for Markov State Modeling of Nonstationary Molecular Dynamics

Multiscale Modeling and Simulation ◽

10.1137/17m1146403 ◽

2018 ◽

Vol 16 (4) ◽

pp. 1455-1485

Author(s):

Péter Koltai ◽

Christof Schütte

Keyword(s):

Molecular Dynamics ◽

Perturbation Expansion ◽

Markov State ◽

Markov State Modeling

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Markov state modeling of sliding friction

Physical Review E ◽

10.1103/physreve.94.053001 ◽

2016 ◽

Vol 94 (5) ◽

Author(s):

F. Pellegrini ◽

François P. Landes ◽

A. Laio ◽

S. Prestipino ◽

E. Tosatti

Keyword(s):

Sliding Friction ◽

Markov State ◽

Markov State Modeling

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Hoogsteen Base Pairing in DNA vs RNA: Thermodynamics and Kinetics from Enhanced Sampling Simulation and Markov State Modeling

Biophysical Journal ◽

10.1016/j.bpj.2019.11.1697 ◽

2020 ◽

Vol 118 (3) ◽

pp. 299a-300a

Author(s):

Dhiman Ray ◽

Ioan Andricioaei

Keyword(s):

Enhanced Sampling ◽

Base Pairing ◽

Thermodynamics And Kinetics ◽

Markov State ◽

Markov State Modeling ◽

Hoogsteen Base Pairing

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Identifying Conformational-Selection and Induced-Fit Aspects in the Binding-Induced Folding of PMI from Markov State Modeling of Atomistic Simulations

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.7b12146 ◽

2018 ◽

Vol 122 (21) ◽

pp. 5649-5656 ◽

Author(s):

Fabian Paul ◽

Frank Noé ◽

Thomas R. Weikl

Keyword(s):

Atomistic Simulations ◽

Induced Fit ◽

Conformational Selection ◽

Markov State ◽

Induced Folding ◽

Markov State Modeling

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Conformational Dynamics of Histone Methyltransferase SET8 Probed by Millisecond-Timescale Molecular Dynamics, Markov State Modeling and Biochemical Experiments

Biophysical Journal ◽

10.1016/j.bpj.2017.11.2203 ◽

2018 ◽

Vol 114 (3) ◽

pp. 398a ◽

Author(s):

Rafal P. Wiewiora ◽

Shi Chen ◽

Minkui Luo ◽

John D. Chodera

Keyword(s):

Molecular Dynamics ◽

Conformational Dynamics ◽

Histone Methyltransferase ◽

Markov State ◽

Markov State Modeling

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Exploring the free energy gain of phase separation via Markov state modeling

The Journal of Chemical Physics ◽

10.1063/1.4994065 ◽

2017 ◽

Vol 147 (3) ◽

pp. 034107

Author(s):

Myra Biedermann ◽

Andreas Heuer

Keyword(s):

Free Energy ◽

Phase Separation ◽

Energy Gain ◽

Markov State ◽

Markov State Modeling

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Transition Paths of Met-Enkephalin from Markov State Modeling of a Molecular Dynamics Trajectory

The Journal of Physical Chemistry B ◽

10.1021/jp412130d ◽

2014 ◽

Vol 118 (11) ◽

pp. 2883-2895 ◽

Author(s):

Rahul Banerjee ◽

Robert I. Cukier

Keyword(s):

Molecular Dynamics ◽

Markov State ◽

Molecular Dynamics Trajectory ◽

Transition Paths ◽

Markov State Modeling

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Complete Coupled Binding–Folding Pathway of the Intrinsically Disordered Transcription Factor Protein Brinker Revealed by Molecular Dynamics Simulations and Markov State Modeling

Biochemistry ◽

10.1021/acs.biochem.8b00441 ◽

2018 ◽

Vol 57 (30) ◽

pp. 4404-4420 ◽

Author(s):

Andrew P. Collins ◽

Peter C. Anderson

Keyword(s):

Molecular Dynamics ◽

Transcription Factor ◽

Molecular Dynamics Simulations ◽

Folding Pathway ◽

Intrinsically Disordered ◽

Markov State ◽

Markov State Modeling ◽

Dynamics Simulations

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Mapping pH-Dependent State Transitions of a Pentameric Ligand-gated Ion Channel through Markov State Modeling

Biophysical Journal ◽

10.1016/j.bpj.2019.11.1160 ◽

2020 ◽

Vol 118 (3) ◽

pp. 191a

Author(s):

Cathrine Bergh ◽

Laura Orellana ◽

Stephanie A. Heusser ◽

Rebecca J. Howard ◽

Erik Lindahl

Keyword(s):

Ion Channel ◽

State Transitions ◽

Markov State ◽

Ph Dependent ◽

Markov State Modeling ◽

Dependent State

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